Using Permanova in JMP

I'm trying to run a PERMANOVA in JMP instead of Qiime to look at the differences in community composition among different microbial samples based on different factors. I'd also love to learn to build PCoa plots in JMP if possible, but this is secondary.

There's nothing built in to JMP directly comparable to http://qiime.org/scripts/compare_categories.html (not in detail at least).But if you are able to give some more details of the variables you have, I'm sure folks will have some suggestions as to how you may proceed using JMP capabilities. Various 'extra' things may be feasible by using JMP's scripting language, but I would not start with that.

I'm attempting to run a PERMANOVA in JMP instead of Qiime to look at the differences in community composition among different microbial samples based on different factors. Most of the factors I would like to test are nominal and ordinal variables.

Ex- Do breast-fed infant microbiomes differ in community composition from formula-fed infants at different ages?

The feeding variable has three nominal categories “Breast,” “Formula” and “Mixture,” and the age group variable has four levels (0-3 mo., 4-7 mo, 8-11 mo or 12+ mo). Specifically I'd like to test if breast fed infants (0-3mo) differ from formula fed infants of the same age group, and so on.

Another variable is an ordinal scale of household cleanliness 0-2.

I would also like to test the analysis of similarity (ANOSIM) if possible.